Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / datamodel / SequenceI.java

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 933f332..72ce22c 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -48,6 +48,10 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
+
   /**
    * Get the display name
    */
@@ -215,10 +219,10 @@ public interface SequenceI extends ASequenceI
    * from 1), or null if no residues are included in the range
    * 
    * @param fromColum
-   *          - first column base 1
+   *          - first column base 1. (0 and negative positions are rounded up)
    * @param toColumn
    *          - last column, base 1
-   * @return
+   * @return null if fromColum>toColumn
    */
   public ContiguousI findPositions(int fromColum, int toColumn);
 
@@ -506,6 +510,12 @@ public interface SequenceI extends ASequenceI
   public List<DBRefEntry> getPrimaryDBRefs();
 
   /**
+   * Answers true if the sequence has annotation for Hidden Markov Model
+   * information content, else false
+   */
+  boolean hasHMMAnnotation();
+
+  /**
    * Returns a (possibly empty) list of sequence features that overlap the given
    * alignment column range, optionally restricted to one or more specified
    * feature types. If the range is all gaps, then features which enclose it are
@@ -542,7 +552,7 @@ public interface SequenceI extends ASequenceI
    * @param c1
    * @param c2
    */
-  public int replace(char c1, char c2);
+  int replace(char c1, char c2);
 
   /**
    * Answers the GeneLociI, or null if not known
@@ -572,7 +582,7 @@ public interface SequenceI extends ASequenceI
    *          the iterator to use
    * @return a String corresponding to the sequence
    */
-  public String getSequenceStringFromIterator(Iterator<int[]> it);
+  String getSequenceStringFromIterator(Iterator<int[]> it);
 
   /**
    * Locate the first position in this sequence which is not contained in an
@@ -582,8 +592,15 @@ public interface SequenceI extends ASequenceI
    *          iterator over regions
    * @return first residue not contained in regions
    */
+
   public int firstResidueOutsideIterator(Iterator<int[]> it);
 
 
+  /**
+   * Answers true if this sequence has an associated Hidden Markov Model
+   * 
+   * @return
+   */
+  boolean hasHMMProfile();
 }